Structure-function analysis of the Z-DNA-binding domain Z alpha of dsRNA adenosine deaminase type I reveals similarity to the (alpha+beta) family of helix-turn-helix proteins

RNA editing alters pre-mRNA through site-selective adenosine deamination, w hich results in codon changes that lead to the production of novel proteins . An enzyme that catalyzes this reaction, double-stranded RNA adenosine dea minase (ADAR1), contains two N-terminal Z-DNA-binding motifs, Z alpha and Z beta, the function of which is as yet unknown. In this study, multidimensi onal NMR spectroscopy was used to show that the topology of Z alpha is alph a 1 beta 1 alpha 2 alpha 3 beta 2 beta 3. Long-range NOEs indicate that bet a 1 and beta 3 interact with each other. Site-directed mutagenesis was used to identify residues in alpha 3, beta 3 and the loop connecting beta 2 to beta 3 that affect Z-DNA binding. Also identified were 11 hydrophobic resid ues that are essential for protein stability. Comparison with known structu res reveals some similarity between Z alpha and (alpha + beta) helix-turn-h elix proteins, such as histone 5 and the family of hepatocyte nuclear facto r-3 winged-helix-turn-helix transcription factors. Taken together, the stru ctural and functional data suggest that recognition of Z-DNA by Z alpha inv olves residues in both the alpha 3 helix and the C-terminal beta-sheet.